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Iron in PDB 4d3b: Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with N1-(2-(1H-Imidazol-1-Yl)Pyrimidin-4-Yl)-N2- (3-Fluorophenethyl)Ethane-1,2-Diamine

Enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with N1-(2-(1H-Imidazol-1-Yl)Pyrimidin-4-Yl)-N2- (3-Fluorophenethyl)Ethane-1,2-Diamine

All present enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with N1-(2-(1H-Imidazol-1-Yl)Pyrimidin-4-Yl)-N2- (3-Fluorophenethyl)Ethane-1,2-Diamine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with N1-(2-(1H-Imidazol-1-Yl)Pyrimidin-4-Yl)-N2- (3-Fluorophenethyl)Ethane-1,2-Diamine, PDB code: 4d3b was solved by H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.873 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.847, 110.456, 164.176, 90.00, 90.00, 90.00
R / Rfree (%) 18.63 / 22.59

Other elements in 4d3b:

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with N1-(2-(1H-Imidazol-1-Yl)Pyrimidin-4-Yl)-N2- (3-Fluorophenethyl)Ethane-1,2-Diamine also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Zinc (Zn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with N1-(2-(1H-Imidazol-1-Yl)Pyrimidin-4-Yl)-N2- (3-Fluorophenethyl)Ethane-1,2-Diamine (pdb code 4d3b). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with N1-(2-(1H-Imidazol-1-Yl)Pyrimidin-4-Yl)-N2- (3-Fluorophenethyl)Ethane-1,2-Diamine, PDB code: 4d3b:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4d3b

Go back to Iron Binding Sites List in 4d3b
Iron binding site 1 out of 2 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with N1-(2-(1H-Imidazol-1-Yl)Pyrimidin-4-Yl)-N2- (3-Fluorophenethyl)Ethane-1,2-Diamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with N1-(2-(1H-Imidazol-1-Yl)Pyrimidin-4-Yl)-N2- (3-Fluorophenethyl)Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe750

b:15.9
occ:1.00
 FE A:HEM750 0.0 15.9 1.0
NC A:HEM750 2.0 10.5 1.0
NA A:HEM750 2.1 16.1 1.0
NB A:HEM750 2.1 19.1 1.0
ND A:HEM750 2.1 16.6 1.0
SG A:CYS415 2.3 16.1 1.0
N01 A:6J0800 2.3 26.9 1.0
C1C A:HEM750 3.0 13.7 1.0
C4C A:HEM750 3.1 9.9 1.0
C4A A:HEM750 3.1 19.2 1.0
C1A A:HEM750 3.1 15.0 1.0
C1B A:HEM750 3.1 20.7 1.0
C4D A:HEM750 3.1 20.4 1.0
C1D A:HEM750 3.1 17.3 1.0
C4B A:HEM750 3.1 23.5 1.0
C02 A:6J0800 3.2 23.3 1.0
CB A:CYS415 3.3 9.2 1.0
C05 A:6J0800 3.4 27.9 1.0
CHD A:HEM750 3.4 19.5 1.0
CHB A:HEM750 3.4 15.5 1.0
CHC A:HEM750 3.4 21.0 1.0
CHA A:HEM750 3.4 15.8 1.0
CA A:CYS415 4.1 11.9 1.0
C2C A:HEM750 4.3 16.9 1.0
C3C A:HEM750 4.3 11.8 1.0
C2A A:HEM750 4.3 14.7 1.0
C3A A:HEM750 4.3 21.9 1.0
C2B A:HEM750 4.3 19.5 1.0
C3D A:HEM750 4.3 17.9 1.0
C3B A:HEM750 4.3 23.1 1.0
C2D A:HEM750 4.3 14.9 1.0
N03 A:6J0800 4.3 23.3 1.0
C04 A:6J0800 4.5 25.2 1.0
NE1 A:TRP409 4.5 19.2 1.0
C A:CYS415 4.8 16.8 1.0
N A:GLY417 4.9 17.8 1.0
N A:VAL416 4.9 17.4 1.0

Iron binding site 2 out of 2 in 4d3b

Go back to Iron Binding Sites List in 4d3b
Iron binding site 2 out of 2 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with N1-(2-(1H-Imidazol-1-Yl)Pyrimidin-4-Yl)-N2- (3-Fluorophenethyl)Ethane-1,2-Diamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with N1-(2-(1H-Imidazol-1-Yl)Pyrimidin-4-Yl)-N2- (3-Fluorophenethyl)Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe750

b:14.8
occ:1.00
 FE B:HEM750 0.0 14.8 1.0
NC B:HEM750 2.0 8.1 1.0
NB B:HEM750 2.0 16.8 1.0
ND B:HEM750 2.1 15.1 1.0
NA B:HEM750 2.1 12.4 1.0
SG B:CYS415 2.3 17.1 1.0
N01 B:6J0800 2.3 25.8 1.0
C1C B:HEM750 3.0 11.0 1.0
C4C B:HEM750 3.0 13.1 1.0
C4B B:HEM750 3.0 17.6 1.0
C1D B:HEM750 3.1 17.5 1.0
C1B B:HEM750 3.1 15.9 1.0
C4D B:HEM750 3.1 17.7 1.0
C1A B:HEM750 3.1 8.9 1.0
C4A B:HEM750 3.1 16.0 1.0
C05 B:6J0800 3.3 25.1 1.0
C02 B:6J0800 3.3 21.0 1.0
CB B:CYS415 3.3 9.4 1.0
CHC B:HEM750 3.3 14.9 1.0
CHD B:HEM750 3.4 16.4 1.0
CHB B:HEM750 3.5 16.2 1.0
CHA B:HEM750 3.5 12.2 1.0
CA B:CYS415 4.1 8.8 1.0
C2C B:HEM750 4.2 10.6 1.0
C3C B:HEM750 4.2 9.8 1.0
C3B B:HEM750 4.2 19.8 1.0
C2B B:HEM750 4.3 17.8 1.0
C2D B:HEM750 4.3 19.4 1.0
C3D B:HEM750 4.3 16.8 1.0
C2A B:HEM750 4.3 16.5 1.0
C3A B:HEM750 4.3 15.2 1.0
N03 B:6J0800 4.4 24.9 1.0
NE1 B:TRP409 4.5 17.2 1.0
C04 B:6J0800 4.5 24.8 1.0
C B:CYS415 4.9 14.3 1.0
O B:HOH2249 4.9 24.4 1.0
N B:GLY417 4.9 19.1 1.0

Reference:

P.Mukherjee, H.Li, I.F.Sevrioukova, G.Chreifi, P.Martasek, L.J.Roman, T.L.Poulos, R.B.Silverman. Novel 2,4-Disubstituted Pyrimidines As Potent, Selective, and Cell-Permeable Inhibitors of Neuronal Nitric Oxide Synthase. J.Med.Chem. 2014.
ISSN: ESSN 1520-4804
PubMed: 25489882
DOI: 10.1021/JM501719E
Page generated: Tue Aug 5 09:44:19 2025

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